It was not immediately clear whether the vote had the force of law.
Legislators in the upper house of the country's reconvened former parliament on Thursday voted 44-0 with two abstentions to name Ishenbai Kadyrbekov president.
The lower chamber did not immediately approve the choice, which lawmakers in the body said needed their approval under the law.
An upper house member, Temir Sariyev, said "nobody knows what is legitimate right now."
The late-night vote came as politicians scrambled to set up legitimate bodies of power after protesters seized the government headquarters and drove Akayev out of power, and to restore order amid looting in the capital, Bishkek.
Kadyrbekov, a Communist lawmaker in the previous bicameral parliament, was disqualified by authorities from running in the disputed elections in February and early March, which fuelled the protests.
"Nobody knows what is legitimate right now"
upper house member
The lawmakers also named Felix Kulov, a popular opposition leader who was released from prison on Thursday, to be in charge of law enforcement agencies.
The MPs also told the Coordinating Council of National Unity, headed by prominent opposition leader Kurmanbek Bakiyev, to make nominations for government posts by Friday morning.
The lawmakers voted no-confidence in Akayev's government.
Bakiyev had earlier said that Prime Minister Nikolai Tanayev resigned, but that the law enforcement, defence and security ministries were working with the opposition.